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| Software | Python2 Version | Python3 Version | Description | in devel_tools |
|---|---|---|---|---|
| all-dev | y | |||
| blaze | 0.10.1 | 0.10.1 | An interface to query data on different storage systems | y |
| cutadapt | 1.18 | 1.18 | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
| dendropy | phylogenetic computing | y | ||
| freetype-dev (libfreetype6-dev) | This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library. | y | ||
| leukgen-disambiguate | 1.0.1 | 1.0.1 | Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0. | y |
| MACS2 | 2.1.2 | Model Based Analysis for ChIP-Seq data | y | |
| maplot | 1.0.2 | 1.0.2 | Python package for creating interactive MA-plots | y |
| matplotlib | 2.1.1 | 3.2.1 | python 2D plotting library | y |
| networkx | 2.2 | 2.0 | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
| nimfa | 1.3.4 | 1.3.4 | Nonnegative matrix factorization | y |
| numpy | 1.13.3 | 1.13.3 | scientific computing with Python | y |
| pandas | 0.22.0 | 0.22.0 | Python Data Analysis Library | y |
| patsy | 0.4.1+dev | 0.2.1 | Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design matrices. Patsy brings the convenience of R “formulas” to Python. | y |
| pip | Python installation program (to install python modules) | y | ||
| plotly | 4.0.0 | 4.0.0 | An open-source, interactive data visualization library for Python | y |
| pysam | 0.8.4 | 0.8.4 | a python module for reading, manipulating and writing genomic data sets | y |
| pyvttbl | 0.5.2.2 | 0.5.2.2 | Multidimensional pivot tables, data processing, statistical computation | y |
| reportlab (->biopython?) | 3.4.0 (->1.70) | 3.5.12 (->1.73) | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. (→ Freely available tools for computational molecular biology) | y |
| rpy2 | 2.8.6 | 2.9.2 | Python interface to R | y |
| seaborn | 0.8.1 | 0.8.1 | statistical data visualization | y |
| scipy | 0.19.1 | 0.19.1 | Collection of Python software for mathematics, science, and engineering. | y |
| sklearn | Machine Learning in Python | y | ||
| skimage | Image processing in Python | y | ||
| statsmodels | 0.8.0 | 0.8.0 | Estimation of statistical models | y |
| pytorch/torch | ||||
torchvision |
Additional R Tools
(cqbhiera/common.yaml dont appear to have versions)
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| Software | Description | Path | in molecular_structures_client.pp |
|---|---|---|---|
| mgltools |
Other software Packages
| Software | Descripition | Path | puppet file |
|---|---|---|---|
| tensorflow | platform for machine learning | ||
| keras | high-level API of TensorFlow |
POD-specific software (look for these)
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